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graph_util.py
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graph_util.py
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import re
import sys
def parserFile(filename):
readnumber = re.compile('[r]+\d+')
line_spliter = re.compile('\t+')
colon_spliter = re.compile(':')
forward_reads = 0
reverse_reads = 0
unmatched_reads = 0
read_quality = [[]]
match_scores = []
#TODO throw an error/ warning if the readSize is greater than the number
#of lines in the file.
f = open(filename)
#Splitting everyline into its own place in the arry
lines = f.readlines()
#Itterating though everyline
for i in range(3, len(lines)):
get_match_score = True
#Splitting the lines into whitespace
subline = line_spliter.split(lines[i])
if (subline[1] == '0'):
forward_reads += 1
elif (subline[1] =='16'):
reverse_reads += 1
else:
unmatched_reads += 1
get_match_score = False
for j in range(len(subline[10])):
while(len(read_quality) < len(subline[10])):
read_quality.append([])
read_quality[j].append(subline[10][j])
if (get_match_score):
match_scores.append(int(colon_spliter.split(subline[11])[2]))
read_quality = read_quality_converter(read_quality)
return (forward_reads, reverse_reads, unmatched_reads, read_quality, match_scores)
def matched_vs_unmatched_pie_chart(forward_reads, reverse_reads, unmatched_reads):
match_chart_labels = ['Forward Reads(Matched)', 'Reverse Reads (Matched)', 'Unmatched Reads']
match_chart_values = [forward_reads, reverse_reads, unmatched_reads]
return (match_chart_labels, match_chart_values)
def phred33_to_q(qual):
#Turn Phred+33 ASCII-encoded quality into Phred-scaled integer
return ord(qual)-33
def read_quality_converter(read_quality):
for i in range(len(read_quality)):
for j in range(len(read_quality[i])):
#Converting the read quality data to probabilities
read_quality[i][j] = phred33_to_q(read_quality[i][j])
return read_quality
def make_data_for_box_plot(read_quality):
data = [[]]
for i in range(len(read_quality)):
data.append(read_quality[i])
return data
def parseString(txt):
spliter = re.compile('\n+')
readnumber = re.compile('[r]+\d+')
line_spliter = re.compile('\t+')
colon_spliter = re.compile(':')
forward_reads = 0
reverse_reads = 0
unmatched_reads = 0
tlen = []
read_quality_unpaired = [[]]
read_quality_first = [[]]
read_quality_second = [[]]
match_scores = []
mapq_scores = []
lines = spliter.split(txt)
#Itterating though everyline
for i in range(len(lines) - 1):
get_match_score = True
subline = line_spliter.split(lines[i])
if (int(subline[1]) & 4 == 4):
unmatched_reads += 1
get_match_score = False
elif (int(subline[1]) & 16 == 16):
reverse_reads += 1
else:
forward_reads += 1
if(int(subline[1]) & 2 == 2): #read is paired
tlen.append(abs(int(subline[8])))
if(int(subline[1]) & 64 == 64):
for j in range(len(subline[10]) - 1):
while(len(read_quality_first) < len(subline[10])):
read_quality_first.append([])
read_quality_first[j].append(subline[10][j])
elif(int(subline[1]) & 128 == 128):
for j in range(len(subline[10]) - 1):
while(len(read_quality_second) < len(subline[10])):
read_quality_second.append([])
read_quality_second[j].append(subline[10][j])
else: #read is unpaired
for j in range(len(subline[10]) - 1):
while(len(read_quality_unpaired) < len(subline[10])):
read_quality_unpaired.append([])
read_quality_unpaired[j].append(subline[10][j])
if (get_match_score):
match_scores.append(int(colon_spliter.split(subline[11])[2]))
mapq_scores.append(int(subline[4]))
# except:
# print("Invalid Line")
read_quality_unpaired = read_quality_converter(read_quality_unpaired)
read_quality_first = read_quality_converter(read_quality_first)
read_quality_second = read_quality_converter(read_quality_second)
return (forward_reads, reverse_reads, unmatched_reads, read_quality_unpaired, read_quality_first, read_quality_second, match_scores, tlen, mapq_scores)
def parseAlignmentSummary(txt):
sys.stderr.write(txt)
spliter = re.compile('\n+')
line_spliter = re.compile('\s+')
summary_finder = re.compile('\d+\sreads;\sof\sthese:')
sys.stderr.write(summary_finder.split(txt)[-1])
if summary_finder.search(txt):
txt = summary_finder.split(txt)[-1]
lines = spliter.split(txt)
unaligned = int(line_spliter.split(lines[2])[1])
aligned = int(line_spliter.split(lines[3])[1])
multi_aligned = int(line_spliter.split(lines[4])[1])
return (unaligned, aligned, multi_aligned)
def matched_vs_unmatched_pie_chart(forward_reads, reverse_reads, unmatched_reads):
match_chart_labels = ['Forward Reads(Matched)', 'Reverse Reads (Matched)', 'Unmatched Reads']
match_chart_values = [forward_reads, reverse_reads, unmatched_reads]
return (match_chart_labels, match_chart_values)
def phred33_to_q(qual):
#Turn Phred+33 ASCII-encoded quality into Phred-scaled integer
return ord(qual)-33
def read_quality_converter(read_quality):
for i in range(len(read_quality)):
for j in range(len(read_quality[i])):
#Converting the read quality data to probabilities
read_quality[i][j] = phred33_to_q(read_quality[i][j])
return read_quality
def make_data_for_box_plot(read_quality):
data = [[]]
for i in range(len(read_quality)):
data.append(read_quality[i])
return data